I am facing the scenario as below whenever I try to hide the Desktop Icon for Ubuntu 13.10.

When my default File Manager is set to Nautilus, everything is working fine even after I set the Desktop Icon to "Hide" from Ubuntu Tweak tool.

Problem is when I set my default File Manager (xdg-mime default nemo.desktop inode/directory application/x-gnome-saved-search) to either Nemo or Caja, whenever the file manager start, the Desktop will be shown with icon and I will need to manually kill the file manager process for the Desktop Icon to be hidden again.